git:20260929.2b7013d to git:20260930.913abeb

25 added, 211 removed. Audit A to A.

---

name: manage-project

description: "Research project management for medical manuscripts. Scaffold project structure, track writing progress across phases, maintain project memory files, generate submission checklists and backwards timelines. Commands: init, status, sync-memory, checklist, timeline."

triggers: manage project, project init, project status, submission checklist, project scaffold, create project, new paper project

tools: Read, Write, Edit, Bash, Grep, Glob

model: inherit

---

# Manage-Project Skill -- Research Project Management

- ## Purpose

- Scaffold new research projects, track manuscript writing progress, maintain lightweight project memory, generate pre-submission checklists, and create backwards submission timelines. Integrates with all other writing skills and the project-manager agent.

- ---

## Commands

### `/manage-project init {name} --type {type} --journal {journal} [--ssot] [--zotero-collection NAME]`

- Create a complete project scaffold for a new research paper.

**Parameters:**

- `{name}` -- Project identifier (e.g., `nnunet-skull-fracture`, `rfa-meta-analysis`)

- `--ssot` -- Emit `SSOT.yaml` (schema v1) from `templates/SSOT.yaml.template` instead of legacy `project.yaml`. Required for Phase 1C auto-enforce (the PostToolUse verify-refs hook blocks instead of warns). New projects should pass `--ssot`; legacy in-flight projects stay on `project.yaml` until `/manage-project migrate-ssot` is run.

- - `--zotero-collection NAME` -- Optional. Create a Zotero collection via pyzotero and populate `library_id` + `collection_key` in the contract. Requires `ZOTERO_API_KEY` + `ZOTERO_LIBRARY_ID` (optionally `ZOTERO_LIBRARY_TYPE`, default `user`). **Graceful degrade:** with pyzotero missing or credentials absent, the contract is scaffolded with `library_id: null` / `collection_key: null` and a WARN is printed.

+ - `--zotero-collection NAME` -- Optional. Create a Zotero collection via pyzotero and populate `library_id` + `collection_key` in the contract. Requires `ZOTERO_API_KEY` + `ZOTERO_LIBRARY_ID` (optionally `ZOTERO_LIBRARY_TYPE`, default `user`). With pyzotero or the credentials missing, the contract is scaffolded with `library_id: null` / `collection_key: null` and a WARN is printed.

**SSOT template substitutions:** `{{PROJECT_ID}}` → `{name}`; `{{PROJECT_TYPE}}` → the SSOT

`project_type` enum mapped from `--type` (`original → original_research`, `meta → meta_analysis`,

`case → case_report`, `ai_validation → ai_validation`, else `other`). Without

`--zotero-collection`, `library_id` / `collection_key` stay `null` until the owner links an

existing collection.

- **Implementation:** backed by `scripts/init_project.py` in this skill. Invoke it directly when running

- outside the skill harness:

+ Run `scripts/init_project.py`:

```bash

python3 "${CLAUDE_SKILL_DIR}/scripts/init_project.py" \

--name {name} --type {type} --journal {journal} [--ssot] \

--project-root {target_dir}

```

- The helper writes the contract file (`SSOT.yaml` with `--ssot`, else legacy `project.yaml`), the

+ It writes the contract file (`SSOT.yaml` with `--ssot`, else legacy `project.yaml`), the

directory scaffold, the minimal stubs `scripts/validate_project_contract.py` requires

- (`manuscript/index.qmd`, `artifact_manifest.json`, `qc/status.json`), the memory-file templates,

+ (`manuscript/index.qmd`, `artifact_manifest.json`, `qc/status.json`), the memory-file stubs,

and `project_state.json`. **`qc/migration_complete` is NOT written by init** — that marker belongs

to the migrate pipeline.

**Do not hand-build the scaffold.** The script is the source of truth for the tree and for

- `project_state.json`; a hand-built one drifts from what the contract validator expects.

- **Read on demand:**

+ `project_state.json`; a hand-built one drifts from what the contract validator expects. Read

+ `${CLAUDE_SKILL_DIR}/references/init_scaffold.md` only when you need to know where a scaffolded

+ file lands or what a `project_state.json` field means.

- | File | Read it when | Cost if read blindly |

- |---|---|---|

- | `references/init_scaffold.md` | you need to know where a scaffolded file lands, or what a `project_state.json` field means | ~1,400 tokens describing output the script already produces for you |

+ After the script, copy the matching reporting-guideline checklist from

+ `${CLAUDE_SKILL_DIR}/../check-reporting/references/checklists/` into `references/checklist_{GUIDELINE}.md`.

- ---

### `/manage-project migrate-ssot [--no-mark-complete]`

- Thin wrapper over `scripts/migrate_project_to_ssot.py` that converts a legacy `project.yaml` project into SSOT.yaml form and, by default, touches `qc/migration_complete` so Phase 1C `auto` mode switches from `warn` to `enforce`.

+ Converts a legacy `project.yaml` project into SSOT.yaml form and, by default, touches `qc/migration_complete` so Phase 1C `auto` mode switches from `warn` to `enforce`.

```bash

python3 "${CLAUDE_SKILL_DIR}/scripts/migrate_project_to_ssot.py" \

--project-root . --write --mark-complete

```

- - Default: `--write --mark-complete` (enforce-ready).

- - `--no-mark-complete` flag form: run with `--write` only. Use when the project still has open QC failures — enforcement is deferred until the migration is validated.

+ - `--no-mark-complete`: run with `--write` only. Use it when the project still has open QC failures — enforcement is deferred until the migration is validated.

- The migrate script refuses to touch `qc/migration_complete` unless the generated SSOT.yaml passes `validate_project_contract.py` AND `contract_mode=ssot`. Do not `touch qc/migration_complete` manually.

Re-run after resolving failures; the script is idempotent.

- ---

### `/manage-project status`

- Report current progress. Reads `project_state.json`, scans existing files, and checks whether key project memory files are present and aligned.

- **Output format:**

- ```

- ## Project Status: {name}

- Journal: {journal} | Type: {type} | Created: {date}

- Target submission: {date or "not set"}

- ### Phase Progress

- [check] Phase 0: Project Init (complete)

- [check] Phase 1: Outline (complete)

- [check] Phase 2: Tables & Figures (complete)

- [work] Phase 3: Methods (IN PROGRESS)

- [wait] Phase 4: Results (pending)

- [wait] Phase 5: Discussion (pending)

- [wait] Phase 6: Introduction & Abstract (pending)

- [wait] Phase 7: Polish (pending)

- ### Word Counts

- Abstract: 0 / 250 words

- Introduction: 0 / 600 words

- Methods: 847 / 1000 words 85%

- Results: 0 / 900 words

- Discussion: 0 / 800 words

- Total: 847 / 3500 words (journal limit)

- ### Quality Gates

- Critic score (Methods): 87/100 PASS

- Citations verified: 12/12

- Reporting guideline: pending

- ### Project Memory

- PROJECT.md: present

- STATUS.md: stale (last updated 12 days ago)

- CLAIMS.md: missing

- DATA_DICTIONARY.md: present

- ANALYSIS_PLAN.md: missing

- REVIEW_LOG.md: n/a (not in revision)

- ### Next Steps

- 1. Complete Methods draft (150 words remaining)

- 2. Run /analyze-stats for Table 1 and diagnostic accuracy

- 3. Begin Results (Phase 4)

- ```

+ Report current progress: read `project_state.json`, scan the existing files, and check whether the

+ project memory files are present and aligned. Take word-count limits from the target journal's

+ profile, `${CLAUDE_SKILL_DIR}/../write-paper/references/journal_profiles/{JOURNAL}.md`, not from

+ memory. Lay the report out as in `${CLAUDE_SKILL_DIR}/references/status_output_format.md`.

### `/manage-project sync-memory`

- Audit and refresh project memory files so other agents can work with less ambiguity.

- **What it does:**

- - checks for presence of `PROJECT.md`, `STATUS.md`, `CLAIMS.md`, `DATA_DICTIONARY.md`, `ANALYSIS_PLAN.md`, `REVIEW_LOG.md`

- - identifies stale or contradictory project metadata

- - proposes the minimum files to create or update

- - aligns `project_state.json` with the current manuscript phase

- **Suggested use cases:**

- - before handing the project to `project-manager`

- - before a large revision cycle

- - when returning to an old folder after weeks or months

- - when multiple collaborators are editing in parallel

- ---

+ Audit and refresh the project memory files:

+ - check for `PROJECT.md`, `STATUS.md`, `CLAIMS.md`, `DATA_DICTIONARY.md`, `ANALYSIS_PLAN.md`, `REVIEW_LOG.md`

+ - identify stale or contradictory project metadata

+ - propose the minimum files to create or update; create them from `${CLAUDE_SKILL_DIR}/references/scaffold_templates.md`

+ - align `project_state.json` with the current manuscript phase

### `/manage-project checklist`

- Generate a pre-submission checklist covering all quality dimensions.

- **Output:** `submission/pre_submission_checklist.md`

- Read and output the pre-submission checklist from

- `${CLAUDE_SKILL_DIR}/references/pre_submission_checklist.md`.

- ---

+ Read the pre-submission checklist from `${CLAUDE_SKILL_DIR}/references/pre_submission_checklist.md`

+ and write it to `submission/pre_submission_checklist.md`. Then recommend `/self-review` (manuscript

+ quality gate), `/verify-refs` (citation verification) and AI pattern removal (`/write-paper` Phase 7).

### `/manage-project timeline {submission_date}`

- Generate a backwards timeline from submission date.

- **Example:** `/manage-project timeline 2026-05-01`

- **Output:**

- ```

- ## Backwards Timeline to Submission: 2026-05-01

- Week -8 (2026-03-06): Phase 0-2 complete (scaffold, outline, tables)

- Week -7 (2026-03-13): Methods draft -> critic pass

- Week -6 (2026-03-20): Results draft -> critic pass + /analyze-stats complete

- Week -5 (2026-03-27): Discussion draft -> critic pass

- Week -4 (2026-04-03): Introduction + Abstract -> critic pass

- Week -3 (2026-04-10): AI pattern removal + /check-reporting (reporting guideline)

- Week -2 (2026-04-17): /self-review + co-author review

- Week -1 (2026-04-24): Final revisions + figures at 300 DPI + /lit verification

- SUBMISSION (2026-05-01): Upload to journal portal

- Critical path: Statistics must be complete by Week -6.

- Run /analyze-stats as soon as data is available.

- ```

- ---

- ## Project Scaffold Templates

- ### PROJECT.md Template

- ```markdown

- # PROJECT

- - Title:

- - Type:

- - Primary question:

- - Target journal/venue:

- - Lead folder:

- - Collaborators:

- - Last updated:

- ```

- ### STATUS.md Template

- ```markdown

- # STATUS

- - Current stage:

- - Current blocker:

- - Next actions:

- 1.

- 2.

- 3.

- - Last updated:

- ```

- ### CLAIMS.md Template

- ```markdown

- # CLAIMS

- |------|-------------------|---------------------|-----------------|

- | ... | ... | ... | ... |

- ```

- ### DATA_DICTIONARY.md Template

- ```markdown

- # DATA DICTIONARY

- |----------|------------|--------|------|

- | ... | ... | ... | ... |

- ```

- ### ANALYSIS_PLAN.md Template

- ```markdown

- # ANALYSIS PLAN

- - Primary endpoint:

- - Secondary endpoints:

- - Main comparator:

- - Statistical methods:

- - Validation strategy:

- - Sensitivity analyses:

- ```

- ### REVIEW_LOG.md Template

- ```markdown

- # REVIEW LOG

- |------------------|----------------|--------|------------------|

- | ... | ... | ... | ... |

- ```

- ---

- ## Integration with Other Skills

- When called from `/manage-project init`, automatically:

- 1. Load the correct journal profile from `write-paper/references/journal_profiles/{JOURNAL}.md`

- 2. Load the correct paper type template from `write-paper/references/paper_types/{TYPE}.md`

- 3. Copy the appropriate reporting guideline checklist from `check-reporting/references/checklists/`

- 4. Set word count targets based on the journal profile

- After `/manage-project checklist`, recommend calling:

- - `/self-review` for manuscript quality gate

- - `/search-lit` to verify all citations

- - AI pattern removal (built into `/write-paper` Phase 7)

+ Generate a backwards timeline from the submission date, in the layout of

+ `${CLAUDE_SKILL_DIR}/references/timeline_example.md`.

---

## Project State Conventions

**Phase numbers:**

- 0 = Init (scaffold created)

- 1 = Outline approved

- 2 = Table/Figure shells approved

- 3 = Methods (critic >= 85)

- 4 = Results (critic >= 85)

- 5 = Discussion (critic >= 85)

- 6 = Introduction + Abstract (critic >= 85)

- 7 = Polish complete (AI pattern removal + checklist + self-review >= 80)

**Phase status values:** `pending | in_progress | complete | blocked`

- ## Anti-Hallucination

- - **Never fabricate file paths, URLs, DOIs, or package names.** Verify existence before recommending.

- - **Never invent journal metadata, impact factors, or submission policies** without verification at the journal's website.

- - If a tool, package, or resource does not exist or you are unsure, say so explicitly rather than guessing.